diff sens.spec.xml @ 0:78776d48bbad draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sens.spec.xml	Fri May 19 05:38:07 2017 -0400
@@ -0,0 +1,83 @@
+<tool profile="16.07" id="mothur_sens_spec" name="Sens.spec" version="@WRAPPER_VERSION@.0">
+    <description>Determine the quality of OTU assignment</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
+        ## create symlinks to input datasets
+        ln -s "$otu" otu.dat &&
+        ln -s "$dist" dist.dat &&
+
+        echo 'sens.spec(
+            list=otu.dat,
+            #if $dist.is_of_type("mothur.dist"):
+                column=dist.dat,
+            #else
+                phylip=dist.dat,
+            #end if
+            #if $label:
+                label=${ str($label).replace(",","-") },
+            #end if
+            precision=$precision,
+            cutoff=$cutoff,
+            hard=$hard
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
+        <param name="dist" type="data" format="mothur.dist,phylip,tabular" label="phylip,column - Distance Matrix"/>
+        <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" help="By default all are included if no selection is made.">
+            <options>
+                <filter type="data_meta" ref="otu" key="labels"/>
+            </options>
+        </param>
+        <param name="precision" type="integer" value="100" min="0" optional="true" label="precision - Precision for rounding distance values"/>
+        <param name="cutoff" type="float" value="-1" label="cutoff - Distance Cutoff threshold - ignored if not > 0" help="Ignore pairwise distances larger than this, a common value would be 0.10"/>
+        <param name="hard" type="boolean" checked="false" truevalue="true" falsevalue="false" label="hard - Use hard cutoff instead of rounding"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="sensspec" format="tabular" from_work_dir="otu*.sensspec" label="${tool.name} on ${on_string}: sensspec"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
+            <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
+            <output name="sensspec" md5="5eb92a89c4e1fd78c10e5bbe55ee2a7a" ftype="tabular"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test>
+            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
+            <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
+            <param name="cutoff" value="0.10"/>
+            <param name="label" value="0.03,0.05,0.22"/>
+            <output name="sensspec" md5="8e2f46ef59b1ac097a9de2e0ab669bb2" ftype="tabular"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The sens.spec_ command takes a list_ and either a column_  or phylip_ distance matrix to determine the quality of OTU assignment.
+
+
+.. _list: https://www.mothur.org/wiki/List_file
+.. _column: https://www.mothur.org/wiki/Column-formatted_distance_matrix
+.. _phylip: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
+.. _sens.spec: https://www.mothur.org/wiki/Sens.spec
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>